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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
4du82P0Mevalonate diphosphate decarboxylase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
4du82P0Mevalonate diphosphate decarboxylase/1.000
4dpuAGSMevalonate diphosphate decarboxylase/0.569
3qt62P0Mevalonate diphosphate decarboxylase/0.557
4dpy2P0Mevalonate diphosphate decarboxylase/0.533
4q71FADBifunctional protein PutA/0.484
4dptAGSMevalonate diphosphate decarboxylase/0.483
1vbiNADMalate/L-lactate dehydrogenase family protein/0.481
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.481
3tjzGNPADP-ribosylation factor 1/0.479
2q85973UDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.478
4jldADPAdenylate kinase/0.478
1tqf32PBeta-secretase 13.4.23.460.477
4eakATP5'-AMP-activated protein kinase subunit gamma-1/0.477
3c1y2BADNA integrity scanning protein DisA/0.476
4ambDUDPutative glycosyl transferase/0.476
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.474
1m8kNADNicotinamide-nucleotide adenylyltransferase2.7.7.10.473
2iviACWIsopenicillin N synthase1.21.3.10.472
2rlcCHDCholoylglycine hydrolase3.5.1.240.472
4zjuNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.472
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.471
1bwsNDPGDP-L-fucose synthase/0.470
3c212BADNA integrity scanning protein DisA/0.470
4q73FADBifunctional protein PutA/0.470
4f4dCHDFerrochelatase, mitochondrial4.99.1.10.469
1bk0ACVIsopenicillin N synthase1.21.3.10.468
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.468
3h3qH13Collagen type IV alpha-3-binding protein/0.468
4g7gVFVLanosterol 14-alpha-demethylase/0.468
4xguADPPutative pachytene checkpoint protein 2/0.468
2o1sTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.467
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.466
3lqfNADGalactitol dehydrogenase/0.466
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.466
4xr9NADCalS8/0.466
2xtnGTPGTPase IMAP family member 2/0.465
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.464
4cvmANPUDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase/0.464
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.464
1j49NADD-lactate dehydrogenase1.1.1.280.462
2abbFMNPentaerythritol tetranitrate reductase/0.462
3gqvNAPEnoyl reductase LovC10.462
4jnkNAIL-lactate dehydrogenase A chain1.1.1.270.462
4o1mNADEnoyl-acyl carrier reductase/0.461
2ktdPUCProstaglandin-H2 D-isomerase5.3.99.20.460
2oorNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.460
4e5yNDPGDP-L-fucose synthase1.1.1.2710.460
4q72FADBifunctional protein PutA/0.460
2g1n1IGRenin3.4.23.150.459
2gv8NDPThiol-specific monooxygenase1.14.130.459
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.459
3h3t16HCollagen type IV alpha-3-binding protein/0.459
3h86AP5Adenylate kinase/0.459
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.459
3slkNDPPolyketide synthase extender module 2/0.459
4nieNBHNuclear receptor ROR-gamma/0.459
4wdfA2P2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.459
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.458
2dteNAIGlucose 1-dehydrogenase related protein/0.458
2q1uNADPutative nucleotide sugar epimerase/ dehydratase/0.458
3hk1B64Fatty acid-binding protein, adipocyte/0.458
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.458
2d29FADAcyl-CoA dehydrogenase/0.457
3b6zCO7Enoyl reductase LovC10.457
3h3r14HCollagen type IV alpha-3-binding protein/0.457
4rvfTYDD-mycarose 3-C-methyltransferase/0.457
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.457
2fsvNADNAD(P) transhydrogenase subunit alpha part 11.6.1.20.456
2vkeTACTetracycline repressor protein class D/0.456
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.456
3zkyWT4Isopenicillin N synthase1.21.3.10.456
4fryNADPutative signal-transduction protein with CBS domains/0.456
1u2gAPRNAD(P) transhydrogenase subunit alpha part 11.6.1.20.455
3junAJDPhenazine biosynthesis protein A/B/0.455
4fw8NAI3-oxoacyl-(Acyl-carrier-protein) reductase/0.455
4jloADPAdenylate kinase/0.455
1h51FMNPentaerythritol tetranitrate reductase/0.454
1obnASVIsopenicillin N synthase1.21.3.10.454
1uzwCDHIsopenicillin N synthase1.21.3.10.454
1xddAAYIntegrin alpha-L/0.454
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.454
3to6LYS_CMCHistone acetyltransferase ESA1/0.454
4ge90L0Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.454
4xyeNADFormate dehydrogenase/0.454
5eaiFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.454
1h73ANPHomoserine kinase2.7.1.390.453
1kfbIGPTryptophan synthase alpha chain/0.453
1xe65FPPlasmepsin-23.4.23.390.453
1yb5NAPQuinone oxidoreductase1.6.5.50.453
2a92NAIL-lactate dehydrogenase/0.453
4m83ERYOleandomycin glycosyltransferase2.4.10.453
1t2cNAIL-lactate dehydrogenase1.1.1.270.452
2yxuATPPyridoxal kinase2.7.1.350.452
3phiNDPShikimate dehydrogenase (NADP(+))/0.452
4fqsLYAThymidylate synthase ThyA/0.452
4xiwAZMCarbonic anhydrase, alpha type/0.452
5einNAP[LysW]-L-2-aminoadipate 6-phosphate reductase/0.452
1beuIPLTryptophan synthase alpha chain/0.451
2bi4NADLactaldehyde reductase1.1.1.770.451
2gjlFMNNitronate monooxygenase1.13.12.160.451
2npaMMBPeroxisome proliferator-activated receptor alpha/0.451
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.451
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.451
3nxxNDPDihydrofolate reductase1.5.1.30.451
4hwkNAPSepiapterin reductase1.1.1.1530.451
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.451
1b16NAQAlcohol dehydrogenase1.1.1.10.450
1gveNAPAflatoxin B1 aldehyde reductase member 310.450
1hdoNAPFlavin reductase (NADPH)/0.450
1xdpATPPolyphosphate kinase/0.450
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.450
2vbdV10Isopenicillin N synthase1.21.3.10.450
3b2sB2STrichothecene 3-O-acetyltransferase/0.450
3b70NAPEnoyl reductase LovC10.450
3gw9VNILanosterol 14-alpha-demethylase/0.450
3o03NAPDehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase)/0.450
3tqaNDPDihydrofolate reductase/0.450
4b68FADL-ornithine N(5)-monooxygenase/0.450
4bb3KKAIsopenicillin N synthase1.21.3.10.450
4dh60KNBeta-secretase 13.4.23.460.450
4hp8NAP2-deoxy-D-gluconate 3-dehydrogenase/0.450
4yvz3ATDNA integrity scanning protein DisA/0.450
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.450
1dr2TAPDihydrofolate reductase1.5.1.30.449
1h2bNAJNAD-dependent alcohol dehydrogenase/0.449
1m13HYFNuclear receptor subfamily 1 group I member 2/0.449
1p0hACOMycothiol acetyltransferase2.3.1.1890.449
1ty9FMNPhenazine biosynthesis protein PhzG1.40.449
2jb4A14Isopenicillin N synthase1.21.3.10.449
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.449
4oh4ANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.449
1eq2NAPADP-L-glycero-D-manno-heptose-6-epimerase/0.448
1h63FMNPentaerythritol tetranitrate reductase/0.448
1kkq471Peroxisome proliferator-activated receptor alpha/0.448
1zioAP5Adenylate kinase/0.448
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.448
2g1s4IGRenin3.4.23.150.448
3bhiNAPCarbonyl reductase [NADPH] 11.1.1.1840.448
4ipw1G7Mycocyclosin synthase1.14.21.90.448
4m4922YL-lactate dehydrogenase A chain1.1.1.270.448
1ma0NADAlcohol dehydrogenase class-31.1.1.10.447
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.447
1pqc444Oxysterols receptor LXR-beta/0.447
1xe55FEPlasmepsin-23.4.23.390.447
1xkdNAPIsocitrate dehydrogenase [NADP]/0.447
2cmjNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.447
2emuSAHDiphthine synthase/0.447
2i7pACOPantothenate kinase 32.7.1.330.447
2jcxNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.447
2jkvNAP6-phosphogluconate dehydrogenase, decarboxylating1.1.1.440.447
2oapANPType II secretion system protein (GspE-2)/0.447
2qo5CHDFatty acid-binding protein 10-A, liver basic/0.447
3dl0AP5Adenylate kinase/0.447
3p62FMNPentaerythritol tetranitrate reductase/0.447
4g3jVNTLanosterol 14-alpha-demethylase/0.447
5irnADPNucleotide binding oligomerization domain containing 2/0.447
1mj9COAHistone acetyltransferase ESA1/0.446
1qoqIGPTryptophan synthase alpha chain/0.446
1zrqFAD5,10-methylenetetrahydrofolate reductase1.5.1.200.446
2ft9CHDFatty acid-binding protein 2, liver/0.446
2g1r3IGRenin3.4.23.150.446
2uxoTACHTH-type transcriptional regulator TtgR/0.446
2zbaZBATrichothecene 3-O-acetyltransferase/0.446
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.446
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.446
4i1iNADMalate dehydrogenase/0.446
1adfTADAlcohol dehydrogenase E chain1.1.1.10.445
1qlhNADAlcohol dehydrogenase E chain1.1.1.10.445
1yqdNAPSinapyl alcohol dehydrogenase/0.445
2ahrNAPPyrroline-5-carboxylate reductase/0.445
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.445
2ftoCB3Thymidylate synthase/0.445
2wqpWQPPolysialic acid capsule biosynthesis protein SiaC/0.445
2y0mACOHistone acetyltransferase KAT8/0.445
3axkNDPRibulose bisphosphate carboxylase large chain4.1.1.390.445
3d8vUD1Bifunctional protein GlmU/0.445
3p74FMNPentaerythritol tetranitrate reductase/0.445
3td7FADProbable FAD-linked sulfhydryl oxidase R5961.8.3.20.445
4a6nFADTetX family tetracycline inactivation enzyme/0.445
4cdmFO1Deoxyribodipyrimidine photolyase/0.445
4jkyADPAdenylate kinase/0.445
4ktoFADPutative isovaleryl-CoA dehydrogenase protein/0.445
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.445
1mjaCOAHistone acetyltransferase ESA1/0.444
1mjbACOHistone acetyltransferase ESA1/0.444
1rfuADPPyridoxal kinase2.7.1.350.444
2a94AP0L-lactate dehydrogenase1.1.1.270.444
2rcyNAPPyrroline-5-carboxylate reductase/0.444
2zatNAPDehydrogenase/reductase SDR family member 41.1.1.1840.444
3atzFMNProstaglandin F2a synthase/0.444
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.444
3d4pNADL-lactate dehydrogenase 11.1.1.270.444
3g5hYTTMycocyclosin synthase1.14.21.90.444
3m6iNADL-arabinitol 4-dehydrogenase1.1.1.120.444
3tr05GPGuanylate kinase/0.444
3tzaTZGGlutamate receptor 2/0.444
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.444
4trnNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.444
1njfADPDNA polymerase III subunit tau2.7.7.70.443
2aqiNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.443
2i4qUA4Renin3.4.23.150.443
2po7CHDFerrochelatase, mitochondrial4.99.1.10.443
2q1sNAIPutative nucleotide sugar epimerase/ dehydratase/0.443
2x7hPFNProstaglandin reductase 310.443
3bv2P38Mitogen-activated protein kinase 14/0.443
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.443
3gwfNAPCyclohexanone monooxygenase/0.443
3hazFADBifunctional protein PutA/0.443
3ijdC2FMethylenetetrahydrofolate reductase/0.443
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4a802ANMajor pollen allergen Bet v 1-A/0.443
4a8v2ANMajor pollen allergen Bet v 1-J/0.443
4an4DUDPutative glycosyl transferase/0.443
4dbzNDPPutative ketoacyl reductase1.3.10.443
4k6fNAPPutative Acetoacetyl-CoA reductase/0.443
5hwsNAP2-dehydropantoate 2-reductase/0.443
1ju2FAD(R)-mandelonitrile lyase 24.1.2.100.442
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.442
1thyUMPThymidylate synthase/0.442
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.442
2ien017Gag-Pol polyprotein3.4.23.160.442
2ql6ADPNicotinamide riboside kinase 1/0.442
2rh9IGPTryptophan synthase alpha chain/0.442
3a3gDLZLumazine protein/0.442
3c35KAIGlutamate receptor ionotropic, kainate 1/0.442
3iaaTYDCalG2/0.442
3nsh957Beta-secretase 13.4.23.460.442
3qv1NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic1.2.1.130.442
4bfxZVXPantothenate kinase2.7.1.330.442
4dfg0JVGag-Pol polyprotein3.4.23.160.442
4i0i957Beta-secretase 13.4.23.460.442
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.442
1dg8NDPDihydrofolate reductase1.5.1.30.441
1dirNADDihydropteridine reductase1.5.1.340.441
1i59ANPChemotaxis protein CheA2.7.13.30.441
1juvNDPDihydrofolate reductase1.5.1.30.441
1kp3ATPArgininosuccinate synthase6.3.4.50.441
2eeqSAHDiphthine synthase/0.441
2g20L1ARenin3.4.23.150.441
2i7nACOPantothenate kinase 12.7.1.330.441
2owuSAHDiphthine synthase/0.441
2x0iNAIMalate dehydrogenase/0.441
2x8hFADThioredoxin glutathione reductase/0.441
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.441
3gegNADShort-chain dehydrogenase/reductase SDR/0.441
3qlsNDPDihydrofolate reductase1.5.1.30.441
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.441
4jb1NAPUDP-N-acetylenolpyruvoylglucosamine reductase/0.441
4kzoNAPIsocitrate dehydrogenase [NADP] cytoplasmic1.1.1.420.441
4yxm2BADNA integrity scanning protein DisA/0.441
5ao1DG3Deoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.441
1dxoFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.440
1ha3MAUElongation factor Tu-A/0.440
1hkuNADC-terminal-binding protein 11.1.10.440
1ib6NADMalate dehydrogenase/0.440
2avvMK1Gag-Pol polyprotein3.4.23.160.440
2bu9HFVIsopenicillin N synthase1.21.3.10.440
2g226IGRenin3.4.23.150.440
2ifaFMNUncharacterized protein/0.440
2w3bNDPDihydrofolate reductase1.5.1.30.440
2x06NADL-sulfolactate dehydrogenase/0.440
2y60M8FIsopenicillin N synthase1.21.3.10.440
2y8lADP5'-AMP-activated protein kinase subunit gamma-1/0.440
2ztmNADD(-)-3-hydroxybutyrate dehydrogenase/0.440
3d84NDPDihydrofolate reductase1.5.1.30.440
3ibqATPPyridoxal kinase/0.440
3junAKDPhenazine biosynthesis protein A/B/0.440
3mpjFADGlutaryl-CoA dehydrogenase1.3.99.320.440
3qe0GDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.440
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.440
3zoiM2WIsopenicillin N synthase1.21.3.10.440
4a99FADTetX family tetracycline inactivation enzyme/0.440
4dc0NDPPutative ketoacyl reductase1.3.10.440